1
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Lin SN, Qin L, Taris KKH, Wuite GJL, Dame RT. Unravelling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy. Methods Mol Biol 2024; 2819:519-534. [PMID: 39028522 DOI: 10.1007/978-1-0716-3930-6_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Acoustic force spectroscopy (AFS) is a single-molecule micromanipulation technique that uses sound waves to exert force on surface-tethered DNA molecules in a microfluidic chamber. As large numbers of individual protein-DNA complexes are tracked in parallel, AFS provides insight into the individual properties of such complexes as well as their population averages. In this chapter, we describe in detail how to perform AFS experiments specifically on bare DNA, protein-DNA complexes, and how to extract their (effective) persistence length and contour length from force-extension relations.
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Affiliation(s)
- Szu-Ning Lin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands
| | - Liang Qin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kees-Karel H Taris
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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2
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Taris KKH, Kamsma D, Wuite GJL. Single-Cell Measurements Using Acoustic Force Spectroscopy (AFS). Methods Mol Biol 2024; 2694:467-477. [PMID: 37824018 DOI: 10.1007/978-1-0716-3377-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Single-molecule force spectroscopy is a powerful tool to investigate the forces and motions related to interactions of biological molecules. Acoustic force spectroscopy (AFS) is a developed measurement tool to study single molecules or cells making use of acoustic standing waves. AFS permits high experimental throughput because many individual molecules can be manipulated and tracked in parallel. Moreover, a wide range of forces can be applied as well as a force loading rate with range of six orders of magnitude. At the same time, AFS stands out because of its simplicity and the compactness of the experimental setup. Even though the AFS setup is simple, it can still be challenging to perform high-quality measurements. Here we describe, in detail, how to setup, perform, and analyze an AFS measurement to determine cell adhesion.
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Affiliation(s)
- Kees-Karel H Taris
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Kamsma
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- LUMICKS B.V, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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3
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Sion E, Ab-Rahim S, Muhamad M. Trends on Human Norovirus Virus-like Particles (HuNoV-VLPs) and Strategies for the Construction of Infectious Viral Clones toward In Vitro Replication. Life (Basel) 2023; 13:1447. [PMID: 37511822 PMCID: PMC10381778 DOI: 10.3390/life13071447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/30/2023] Open
Abstract
Most acute gastroenteritis (AGE) outbreaks and sporadic cases in developing countries are attributable to infection by human norovirus (HuNoV), the enteric virus mainly transmitted via fecal-contaminated water. However, it has been challenging to study HuNoV due to the lack of suitable systems to cultivate and replicate the virus, hindering the development of treatments and vaccines. Researchers have been using virus-like particles (VLPs) and infectious viral clones to overcome this challenge as alternatives to fresh virus isolates in various in vitro and ex vivo models. VLPs are multiprotein structures that mimic the wild-type virus but cannot replicate in host cells due to the lack of genetic materials for replication, limiting downstream analysis of the virus life cycle and pathogenesis. The development of in vitro cloning systems has shown promise for HuNoV replication studies. This review discusses the approaches for constructing HuNoV-VLPs and infectious viral clones, the techniques involved, and the challenges faced. It also highlights the relationship between viral genes and their protein products and provides a perspective on technical considerations for producing efficient HuNoV-VLPs and infectious viral clones, which could substitute for native human noroviruses in future studies.
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Affiliation(s)
- Emilly Sion
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Selangor Branch, Sungai Buloh Campus, Sungai Buloh 47000, Selangor, Malaysia
| | - Sharaniza Ab-Rahim
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Selangor Branch, Sungai Buloh Campus, Sungai Buloh 47000, Selangor, Malaysia
| | - Mudiana Muhamad
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Universiti Teknologi MARA, Selangor Branch, Sungai Buloh Campus, Sungai Buloh 47000, Selangor, Malaysia
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4
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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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5
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Silvani G, Romanov V, Martinac B. Sounding a New Era in Biomechanics with Acoustic Force Spectroscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1436:109-118. [PMID: 36571699 DOI: 10.1007/5584_2022_757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The acoustic force spectroscopy (AFS) tool was recently introduced as a novel tool for probing mechanical properties of biomolecules, expanding the application of sound waves to high-throughput quantification of the mechanical properties of single cells. By using controlled acoustic forces in the piconewton to nanonewton range, tens to hundreds of cells functionalized by attached microspheres can simultaneously be stretched and tracked in real-time with sub millisecond time response. Since its first application, several studies have demonstrated the potential and versatility of the AFS for high-throughput measurements of force-induced molecular mechanisms, revealing insight into cellular biomechanics and mechanobiology at the molecular level. In this chapter, we describe the operation of the AFS starting with the underlying physical principles, followed by a run-down of experimental considerations, and finally leading to applications in molecular and cellular biology.
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Affiliation(s)
- Giulia Silvani
- School of Material Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Valentin Romanov
- Victor Chang Cardiac Research Institute, Lowy Packer Building, Darlinghurst, NSW, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Lowy Packer Building, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
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6
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Mizrahi I, Bruinsma R, Rudnick J. Spanning tree model and the assembly kinetics of RNA viruses. Phys Rev E 2022; 106:044405. [PMID: 36397584 DOI: 10.1103/physreve.106.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/17/2022] [Indexed: 06/16/2023]
Abstract
Single-stranded RNA (ssRNA) viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral genome molecules must be selected from a large pool of very similar host messenger RNA molecules and it is not known whether this also can be understood by free energy minimization. We address this question using a simple mathematical model, the spanning tree model, that was recently proposed for the assembly of small ssRNA viruses. We present a statistical physics analysis of the properties of this model. RNA selection takes place via a kinetic mechanism that operates during the formation of the nucleation complex and that is related to Hopfield kinetic proofreading.
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Affiliation(s)
- Inbal Mizrahi
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
| | - Robijn Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Joseph Rudnick
- Department of Physics and Astronomy, University of California, Los Angeles, California 90095, USA
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7
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Kler S, Zalk R, Upcher A, Kopatz I. Packaging of DNA origami in viral capsids: towards synthetic viruses. NANOSCALE 2022; 14:11535-11542. [PMID: 35861608 DOI: 10.1039/d2nr01316a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report a new type of nanoparticle, consisting of a nucleic acid core (>7500 nt) folded into a 35 nm DNA origami sphere, encapsulated by a capsid composed of all three SV40 virus capsid proteins. Compared to the prototype reported previously, whose capsid consists of VP1 only, the new nanoparticle closely adopts the unique intracellular pathway of the native SV40, suggesting that the proteins of the synthetic capsid retain their native viral functionality. Some of the challenges in the design of such near-future composite drugs destined for gene delivery are discussed.
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Affiliation(s)
| | - Ran Zalk
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
| | - Alexander Upcher
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel.
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8
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Determination of protein-protein interactions at the single-molecule level using optical tweezers. Q Rev Biophys 2022; 55:e8. [PMID: 35946323 DOI: 10.1017/s0033583522000075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (koff, kon), affinity values (KD), energy to the transition state ΔG≠, distance to the transition state Δx≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.
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9
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Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
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Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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10
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Lu Y, Shi Y, You J. Strategy and clinical application of up-regulating cross presentation by DCs in anti-tumor therapy. J Control Release 2021; 341:184-205. [PMID: 34774890 DOI: 10.1016/j.jconrel.2021.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/20/2022]
Abstract
The cross presentation of exogenous antigen (Ag) by dendritic cells (DCs) facilitates a diversified mode of T-cell activation, orchestrates specific humoral and cellular immunity, and contributes to an efficient anti-tumor immune response. DCs-mediated cross presentation is subject to both intrinsic and extrinsic factors, including the homing and phenotype of DCs, the spatiotemporal trafficking and degradation kinetics of Ag, and multiple microenvironmental clues, with many details largely unexplored. Here, we systemically review the current mechanistic understanding and regulation strategies of cross presentation by heterogeneous DC populations. We also provide insights into the future exploitation of DCs cross presentation for a better clinical efficacy in anti-tumor therapy.
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Affiliation(s)
- Yichao Lu
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Yingying Shi
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Jian You
- College of Pharmaceutical Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China.
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11
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Buzón P, Maity S, Christodoulis P, Wiertsema MJ, Dunkelbarger S, Kim C, Wuite GJ, Zlotnick A, Roos WH. Virus self-assembly proceeds through contact-rich energy minima. SCIENCE ADVANCES 2021; 7:eabg0811. [PMID: 34730996 PMCID: PMC8565845 DOI: 10.1126/sciadv.abg0811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 kBT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | | | - Monique J. Wiertsema
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Steven Dunkelbarger
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Christine Kim
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Gijs J.L. Wuite
- Physics of Living Systems, Vrije Universiteit, Amsterdam, Netherlands
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
- Corresponding author.
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12
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Zhang W, Jia Q, Teng Y, Yang M, Zhang H, Zhang XE, Wang P, Ge J, Cao S, Li F. An Ultrastable Virus-Like Particle with a Carbon Dot Core and Expanded Sequence Plasticity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101717. [PMID: 34302443 DOI: 10.1002/smll.202101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/06/2021] [Indexed: 06/13/2023]
Abstract
Ordered bio-inorganic hybridization has evolved for the generation of high-performance materials in living organisms and inspires novel strategies to design artificial hybrid materials. Virus-like particles (VLPs) are attracting extensive interest as self-assembling systems and platforms in the fields of biotechnology and nanotechnology. However, as soft nanomaterials, their structural stability remains a general and fundamental problem in various applications. Here, an ultrastable VLP assembled from the major capsid protein (VP1) of simian virus 40 is reported, which contains a carbon dot (C-dot) core. Co-assembly of VP1 with C-dots led to homogeneous T = 1 VLPs with a fourfold increase in VLP yields. The resultant hybrid VLPs showed markedly enhanced structural stability and sequence plasticity. C-dots and a polyhistidine tag fused to the inner-protruding N-terminus of VP1 contributed synergistically to these enhancements, where extensive and strong noncovalent interactions on the C-dot/VP1 interfaces are responsible according to cryo-EM 3D reconstruction, molecular simulation, and affinity measurements. C-dot-enhanced ultrastable VLPs can serve as a new platform, enabling the fabrication of new architectures for bioimaging, theranostics, nanovaccines, etc. The hybridization strategy is simple and can easily be extended to other VLPs and protein nanoparticle systems.
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Affiliation(s)
- Wenjing Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyan Jia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yibo Teng
- Wuhan Ready science and technology corporation Ltd, Wuhan, 430064, China
| | - Mengsi Yang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-En Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Pengfei Wang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jiechao Ge
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Sheng Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Khalesi Moghaddam R, Bhalla N, Q Shen A, Natale G. Deterministic particle assembly on nanophotonic chips. J Colloid Interface Sci 2021; 603:259-269. [PMID: 34214719 DOI: 10.1016/j.jcis.2021.06.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/14/2021] [Accepted: 06/20/2021] [Indexed: 10/21/2022]
Abstract
HYPOTHESIS Controlled particle assembly from a dilute suspension droplet is challenging yet important for many lab-on-a-chip and biosensing applications. The formation of hot spots on the localized surface plasmonic resonance (LSPR) substrates induced by laser excitation can generate microbubbles. These microbubbles, upon the laser removal, shrink and collapse due to electron energy dissipation, leading to guided particle assembly on the LSPR substrate. EXPERIMENTS After depositing dilute silica particles dispersions on both nanoisland (AuNI) and planar gold (Au) plasmonic substrates (referred to as LSPR and SPR substrates respectively), microbubbles were formed when a laser beam was applied. Particle dispersion concentration, laser power, and the radius of circular laser sequence were varied to produce different sizes of particle clusters on the LSPR substrate after bubble shrinkage upon the laser removal. To stabilize the assembled structures over time, sodium chloride (NaCl) was ad ded to the dispersions. FINDINGS Even though thermo-plasmonic flow and microbubbles can be produced with SPR substrates, particle assembly is only possible on LSPR substrates because of electron energy dissipation via nanoscale air gaps trapped in the LSPR substrate. By tuning the laser power, the radius of the circular laser sequence, and the particle dispersion concentration, the number of particles in the assembled structure can be controlled. The addition of NaCl to the dispersion can screen the electrostatic charges among the particles and between the particles and substrate, favoring hydrogen bonding and stabilizing the assembled structures for hours. These findings establish a new framework for utilizing nanophotonic chips where particle assembly can be achieved by a single source of light.
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Affiliation(s)
- Razie Khalesi Moghaddam
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary T2N 1N4, Alberta, Canada
| | - Nikhil Bhalla
- Nanotechnology and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern Ireland, United Kingdom; Heathcare Technology Hub, Ulster University, BT37 0QB Jordanstown, Northern Ireland, United Kingdom
| | - Amy Q Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Giovanniantonio Natale
- Department of Chemical & Petroleum Engineering, University of Calgary, 2500 University Drive NW, Calgary T2N 1N4, Alberta, Canada.
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14
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Le DT, Müller KM. In Vitro Assembly of Virus-Like Particles and Their Applications. Life (Basel) 2021; 11:334. [PMID: 33920215 PMCID: PMC8069851 DOI: 10.3390/life11040334] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Virus-like particles (VLPs) are increasingly used for vaccine development and drug delivery. Assembly of VLPs from purified monomers in a chemically defined reaction is advantageous compared to in vivo assembly, because it avoids encapsidation of host-derived components and enables loading with added cargoes. This review provides an overview of ex cella VLP production methods focusing on capsid protein production, factors that impact the in vitro assembly, and approaches to characterize in vitro VLPs. The uses of in vitro produced VLPs as vaccines and for therapeutic delivery are also reported.
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Affiliation(s)
| | - Kristian M. Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany;
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15
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 2021; 12:1936. [PMID: 33782395 PMCID: PMC8007728 DOI: 10.1038/s41467-021-21953-3] [Citation(s) in RCA: 286] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jason A Wagoner
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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16
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Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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17
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Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021; 3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
Abstract
Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.
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Affiliation(s)
- Robijn F. Bruinsma
- Department of Physics and Astronomy, University of California, Los Angeles, California, USA
| | - Gijs J. L. Wuite
- Fysica van levende systemen, Vrije Universiteit, Amsterdam, the Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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18
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.17.158121. [PMID: 32587966 PMCID: PMC7310622 DOI: 10.1101/2020.06.17.158121] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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19
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Xu C, Zhu W, Mao H, Zhang W, Yin GQ, Zhang XE, Li F. Switch from Polymorphic to Homogenous Self-Assembly of Virus-Like Particles of Simian Virus 40 through Double-Cysteine Substitution. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2004484. [PMID: 33063476 DOI: 10.1002/smll.202004484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/06/2020] [Indexed: 06/11/2023]
Abstract
Self-assembled virus-like particles (VLPs) hold great potential as natural nanomaterials for applications in many fields. For such purposes, monodisperse size distribution is a desirable property. However, the VLPs of simian virus 40 (SV40), a representative VLP platform, are characterized by polymorphism. In an attempt to eliminate the polymorphism, 15 mutants of the VLP subunit (VP1) are constructed through the substitution of double cysteines at the VP1 pentamer interfaces, generating a group of VLPs with altered size distributions. One of the mutants, SS2 (L102C/P300C), specifically forms homogenous T = 1-like tiny VLPs of 24 ± 3 nm in diameter. Moreover, the stability of the SS2 VLPs is markedly enhanced compared with that of wild-type VLPs. The homogeneous self-assembly and stability enhancement of SS2 VLPs can be attributed to the new disulfide bonds contributed by Cys102 and Cys300, which are identified by mass spectrometry and explored by molecular dynamics simulations. Endocytosis inhibition assays indicate that SS2 VLPs, like the polymorphic wild-type VLPs, preserve the multipathway feature of cellular uptake. SS2 VLPs may serve as an evolved version of SV40 VLPs in future studies and applications. The findings of this work would be useful for the design and fabrication of VLP-based materials and devices.
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Affiliation(s)
- Chengchen Xu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, P. R. China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan, 430071, P. R. China
| | - Weiwei Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan, 430071, P. R. China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hanjing Mao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan, 430071, P. R. China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wenjing Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan, 430071, P. R. China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Gen-Quan Yin
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, P. R. China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China
| | - Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences (CAS), Wuhan, 430071, P. R. China
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20
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Valbuena A, Maity S, Mateu MG, Roos WH. Visualization of Single Molecules Building a Viral Capsid Protein Lattice through Stochastic Pathways. ACS NANO 2020; 14:8724-8734. [PMID: 32633498 PMCID: PMC7392527 DOI: 10.1021/acsnano.0c03207] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/26/2020] [Indexed: 05/20/2023]
Abstract
Direct visualization of pathways followed by single molecules while they spontaneously self-assemble into supramolecular biological machines may provide fundamental knowledge to guide molecular therapeutics and the bottom-up design of nanomaterials and nanodevices. Here, high-speed atomic force microscopy is used to visualize self-assembly of the bidimensional lattice of protein molecules that constitutes the framework of the mature human immunodeficiency virus capsid. By real-time imaging of the assembly reaction, individual transient intermediates and reaction pathways followed by single molecules could be revealed. As when assembling a jigsaw puzzle, the capsid protein lattice is randomly built. Lattice patches grow independently from separate nucleation events whereby individual molecules follow different paths. Protein subunits can be added individually, while others form oligomers before joining a lattice or are occasionally removed from the latter. Direct real-time imaging of supramolecular self-assembly has revealed a complex, chaotic process involving multiple routes followed by individual molecules that are inaccessible to bulk (averaging) techniques.
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Affiliation(s)
- Alejandro Valbuena
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Sourav Maity
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Mauricio G. Mateu
- Centro
de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
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21
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Martinac B, Nikolaev YA, Silvani G, Bavi N, Romanov V, Nakayama Y, Martinac AD, Rohde P, Bavi O, Cox CD. Cell membrane mechanics and mechanosensory transduction. CURRENT TOPICS IN MEMBRANES 2020; 86:83-141. [DOI: 10.1016/bs.ctm.2020.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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